He will be replaced by executive vice president David Knox while an international search is undertaken for a permanent CEO, the Adelaide-based major said in a statement this morning.
Santos said Ellice-Flint would continue with the company in a consulting capacity until June 30.
Since his appointment in 2000, Ellice-Flint has taken Santos from a domestic onshore oil and gas producer to become a regional oil and gas field operator and producer of liquefied natural gas and coal seam methane.
He has also been responsible for projects such as the development of the Mutineer and Exeter offshore oil fields, the Bayu Undan LNG field, and recent initiatives such as the Gladstone LNG project, the Moomba Carbon Storage project and the agreement of the South Australian Government to repeal the 15% shareholding cap.
Chairman Stephen Gerlach said Santos had spent the past few months discussing the best timing for the identification and appointment of a new CEO to lead the company's next phase of growth.
"With the shareholding cap soon to be removed and the increasing pace of planning for the Gladstone LNG project, we came to the view that we should implement the orderly transition process announced today," he said.
"John's successor will inherit a company well placed to embark on the next phase of its expansion, as it pursues strategic growth opportunities in new markets."
Gerlach said Knox's extensive industry experience and senior role within Santos meant he was well placed to step into the acting CEO position.
Knox joined Santos last September as executive vice president, growth businesses, where he was responsible for building Santos' emerging new ventures including LNG, geoscience and new ventures, Indonesia and other strategic projects.
Before taking on this role, he was managing director for BP Exploration and Production in Australasia from 2003 to 2007.
He has also previously worked for ARCO and Shell in the United States, Netherlands, United Kingdom and Norway.
He holds a first class Honours degree in mechanical engineering from Edinburgh University, and a Masters of business administration.
